Stereospecific protein-DNA interactions in nucleosomes and nucleosomal arrays of chromatin from primate cells (human, monkey) are studied from the point of view of identifying the structural elements in both the DNA sequences and protein components (histones, nonhistones) accounting for the phasing relationships previously reported. The influence of the experimental variables including ionic strength, temperature and type of nucleases employed in maintaining or destroying the phasing relationships and permitting their detection and detailed analysis will be explored by a variety of techniques, including direct DNA sequencing. The properties and possible functions of a complex family of related primate repetitive DNAs--the alphoid DNAs--are studied by a variety of molecular biological and recombinant DNA techniques to elucidate their role and significance in karyotypic and molecular rearrangements of the primate genomes and their possible consequences for gene expression. Special focus will be on family of interspersed alphoid sequences, the KpnI families, which may be as abundant in primate genomes as the Alu family. A working model suggests that these sequences may bridge the transcribed, coding sequences with which they seem to be associated, and the nontranscribed, highly repetitive sequences, throughout the Primate Order. The purification, properties and sites of DNA cleavage by a site-specific mammalian endonuclease will be studied with the goal of understanding the determinants of its site-specificity, and its possible role in site-specific recombinations or rearrangements that may occur in mammalian cells. The working hypothesis is that the endonuclease is not DNA sequence-specific, but may recognize DNA tertiary structure.